ArticleInternational journal of molecular sciences2016
SAAFEC: Predicting the Effect of Single Point Mutations on Protein Folding Free Energy Using a Knowledge-Modified MM/PBSA Approach.
Article in International journal of molecular sciences, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
45 citing papers in PubMed.
- Stability and Dynamics of the N‑Terminal Domain of TDP-43 and the Effect of Point Mutations.ACS omega · 2026Article
- Role of the Mobile Active Site Flap in IMP Dehydrogenase Inhibitor Binding.ACS infectious diseases · 2025Article
- Review
- Topological deep learning based deep mutational scanning.Computers in biology and medicine · 2023Article
- Predicting the Effect of Single Mutations on Protein Stability and Binding with Respect to Types of Mutations.International journal of molecular sciences · 2023Article
- Biochemical Studies of Systemic Lupus Erythematosus-Associated Mutations in Nonreceptor Tyrosine Kinases Ack1 and Brk.Biochemistry · 2023Article
- LYRUS: a machine learning model for predicting the pathogenicity of missense variants.Bioinformatics advances · 2022Article
- PremPLI: a machine learning model for predicting the effects of missense mutations on protein-ligand interactions.Communications biology · 2021Article
- Computational Investigation of the pH Dependence of Stability of Melanosome Proteins: Implication for Melanosome formation and Disease.International journal of molecular sciences · 2021Article
- A strategy for proline and glycine mutations to proteins with alchemical free energy calculations.Journal of computational chemistry · 2021Article
- SAAMBE-SEQ: a sequence-based method for predicting mutation effect on protein-protein binding affinity.Bioinformatics (Oxford, England) · 2021Article
- Stability Prediction for Mutations in the Cytosolic Domains of Cystic Fibrosis Transmembrane Conductance Regulator.Journal of chemical information and modeling · 2021Article
- Identification of Cytochrome b-245, beta-chain gene mutations, and clinical presentations in Iranian patients with X-linked chronic granulomatous disease.Journal of clinical laboratory analysis · 2021Article
- SAAFEC-SEQ: A Sequence-Based Method for Predicting the Effect of Single Point Mutations on Protein Thermodynamic Stability.International journal of molecular sciences · 2021Article
- Decoding Asymptomatic COVID-19 Infection and Transmission.The journal of physical chemistry letters · 2020Review
- PremPS: Predicting the impact of missense mutations on protein stability.PLoS computational biology · 2020Article
- A novel homozygous variant in an Iranian pedigree with cerebellar ataxia, mental retardation, and dysequilibrium syndrome type 4.Journal of clinical laboratory analysis · 2020Article
- PremPRI: Predicting the Effects of Missense Mutations on Protein-RNA Interactions.International journal of molecular sciences · 2020Article
- Mutations in FAM50A suggest that Armfield XLID syndrome is a spliceosomopathy.Nature communications · 2020Article
- Thr90Ser Mutation in Antithrombin is Associated with Recurrent Thrombosis in a Heterozygous Carrier.Thrombosis and haemostasis · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
unlabelledFolding free energy is an important biophysical characteristic of proteins that reflects the overall stability of the 3D structure of macromolecules. Changes in the amino acid sequence, naturally occurring or made in vitro, may affect the stability of the corresponding protein and thus could be associated with disease. Several approaches that predict the changes of the folding free energy caused by mutations have been proposed, but there is no method that is clearly superior to the others. The optimal goal is not only to accurately predict the folding free energy changes, but also to characterize the structural changes induced by mutations and the physical nature of the predicted folding free energy changes. Here we report a new method to predict the Single Amino Acid Folding free Energy Changes (SAAFEC) based on a knowledge-modified Molecular Mechanics Poisson-Boltzmann (MM/PBSA) approach. The method is comprised of two main components: a MM/PBSA component and a set of knowledge based terms delivered from a statistical study of the biophysical characteristics of proteins. The predictor utilizes a multiple linear regression model with weighted coefficients of various terms optimized against a set of experimental data. The aforementioned approach yields a correlation coefficient of 0.65 when benchmarked against 983 cases from 42 proteins in the ProTherm database. AVAILABILITY: the webserver can be accessed via http://compbio.clemson.edu/SAAFEC/.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.